The successes of AC didn't last long. Directly after the 1998 elections there was an inner-party revolt. Wangcha Rajkumar, who had been elected to the Lok Sabha from the constituency Arunachal East in both 1996 and 1998 considered that Apang had resorted to nepotism when his son was appointed minister. Five state ministers that had sided with Rajkumar were fired by Apang. One of the exministers, Mukut Mithi, split and formed the Arunachal Congress (Mithi). AC(M) was able to gather 40 members of the legislative assembly and Mithi formed a government. Initially both AC and AC(M) supported the Vajpayee government, but since Rajkumar wasn't allotted a ministerial post AC(M) merged with the Indian National Congress ahead of the 1999 elections.

Ahead of the Lok Sabha elections of 1999 AC ran in alliance with BJP]. Omak Apang stood in Arunchal West (came second with 70 760 votes, 30,07% in that constituency). In Arunachal East Rajkumar (now back in INC) defeated the BJP candidate. One reason, its claimed, that the AC-BJP combine fared so badly was that several armed factions (especially the powerful National Socialist Council of Nagaland) in the area worked against them.

The legislative assembly elections same year gave even worse results. AC launched 38 candidates, but only one (Gegong Apang) was elected. In total the party got 68 645 votes (16,68% of the votes in the state).

Ahead of the Lok Sabha elections 2004 the political map of Arunachal Pradesh had been redrawn yet again. July 25, 2003 there was a new split in the INC, and a new party Congress (Dolo) was formed. Apang formed a front called United Democratic Front consisting of himself, Congress (D), an expelled Congress MLA and two independents. In total Apang was able to gather 41 MLAs around gum, and on August 3 Apang was again sworn in as Chief Minister of the state. On August 30 Apang joined BJP] and took with his 41 MLAs. Thus BJP controlled a state government in the North-East for the first time.

Arunachal Congress did however continue to exist as a party even after that the founder Apang had joined BJP.

Ahead of the 2004 Lok Sabha elections AC talked about calling for a boycott, as a protest against that Chakma and Hajong refugees had been given the right to vote in the state. In the end the party did however decide to contest, this time allied with Indian National Congress. AC launched its new party president, Kamen Ringu, in Arunachal West. Ringu came second and got 76 527 votes (34,54% in that constituency). In Arunachal East INC had launched a candidate, that also came second.

In the legislative assembly elections 2004 AC had put up 11 candidates, out of whom two were elected.

The leadership of the party is called Arunachal Congress Working Committee (ACWC).

The organization Arunachal Congress Volunteer Force is probably related to the party.

Just before, 2009 Assembly election, Arunachal Congress merged with Indian National Congress.